From MTZ, mmCIF and .phs data use File -> Open MTZ, CIF or phs.... You can then choose the MTZ columns for the Fourier synthesis. The button “Expert mode” also adds to the options any anomalous columns you may have in the MTZ file (a -90 degree phase shift will be applied). It also provides the option to apply resolution limits.
From a CCP4 map use File -> Read Map. After being generated/read, the map is immediately contoured and centred on the current rotation centre.
This function allows Coot to read an MTZ file and make a map directly (without going through the column selection procedure). The default column labels for auto-reading are "FWT" and "PHWT" for the 2Fo-Fc-style map, "DELFWT" and "PHDELWT" for the difference map. You can change the column labels that Coot uses for auto-reading - here is an example of how to do that:
(set-auto-read-column-labels "2FOFCWT" "PHIWT" 0)
(set-auto-read-column-labels "FOFCWT" "DELPHIWT" 1)
By default the difference map is created in auto-reading the MTZ file. If you don't want a difference map, you can use the function:
(set-auto-read-do-difference-map-too 0)
There are several maps that can be generated from CIF files that contain observed Fs, calculated Fs and calculated phases:
(read-cif-data-with-phases-fo-alpha-calc
cif-file-name) Calculate an atom map using F_obs and
\alpha_calc
(read-cif-data-with-phases-2fo-fc cif-file-name)
Calculate an atom map using F_obs, F_calc and
\alpha_calc
(read-cif-data-with-phases-fo-fc cif-file-name)
Calculate an difference map using F_obs, F_calc and
\alpha_calc.
There are 2 ways to read data by scripting:
(read-phs-and-make-map-using-cell-symm phs-file-name space-group-name a b c alpha beta gamma)
(read-pdb-and-make-map-with-reso-limits imol-previous phs-file-name reso-limit-low reso-limit-high)
The first specifies the cell explicitly, and alpha, beta and gamma are specified in degrees.
The second form allows the specification of resolution limits and takes the cell and symmetry from a previous molecule (typically a pdb file).